1M5X Hydrolase Dna date Jul 10, 2002
title Crystal Structure Of The Homing Endonuclease I-Msoi Bound To Substrate
authors B.Chevalier, M.Turmel, C.Lemieux, R.J.Monnat, B.L.Stoddard
compound source
Molecule: 5'-D(Gpcpapgpapapcpgptpcpgptpgpapg Gptptpcpcpg)-3';
Chain: C
Engineered: Yes
Other_details: Target Dna (Watson Strand)
Synthetic: Yes

Molecule: 5'-D(Cpgpgpapapcptpgptpcptpcpapcpg Tptpcptpgpc)-3';
Chain: D
Engineered: Yes
Other_details: Target Dna (Crick Strand)

Synthetic: Yes

Molecule: Dna Endonuclease I-Msoi
Chain: A, B
Engineered: Yes

Organism_scientific: Monomastix Sp.
Organism_taxid: 141716
Strain: Oke-1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21[De3]
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pi-Msoi
symmetry Space Group: P 1
R_factor 0.219 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.510 42.210 71.320 73.34 73.17 71.09
method X-Ray Diffractionresolution 2.25 Å
ligand CA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • endonuclease activity


  • Primary referenceFlexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI., Chevalier B, Turmel M, Lemieux C, Monnat RJ Jr, Stoddard BL, J Mol Biol 2003 May 30;329(2):253-69. PMID:12758074
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (1m5x.pdb1.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 1M5X
  • CSU: Contacts of Structural Units for 1M5X
  • Likely Quarternary Molecular Structure file(s) for 1M5X
  • Structure Factors (378 Kb)
  • Retrieve 1M5X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1M5X from S2C, [Save to disk]
  • Re-refined 1m5x structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1M5X in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1M5X
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1M5X, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m5xa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1m5xb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1m5x from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1m5x] [1m5x_A] [1m5x_C] [1m5x_B] [1m5x_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 1M5X
  • Community annotation for 1M5X at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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